Starting /dee2/code/volunteer_pipeline.sh ERR6133425 current disk space = 1546825740288 free memory = 1446861772 ERR6133425 SRAfilesize a970f6b7c1a531f4737edd9ab7e01648 ERR6133425.sra ERR6133425.sra file validated ERR6133425 is single end ERR6133425 is conventional basespace ERR6133425 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133425_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.1305 37.0 33.0 37.0 33.0 37.0 2 36.37725 37.0 37.0 37.0 33.0 37.0 3 35.715 37.0 37.0 37.0 33.0 37.0 4 35.511 37.0 37.0 37.0 33.0 37.0 5 35.35725 37.0 37.0 37.0 33.0 37.0 6 35.67025 37.0 37.0 37.0 33.0 37.0 7 37.21375 37.0 37.0 40.0 33.0 40.0 8 37.2915 37.0 37.0 40.0 33.0 40.0 9 37.30725 37.0 37.0 40.0 33.0 40.0 10-11 37.278375 37.0 37.0 40.0 33.0 40.0 12-13 37.2775 37.0 37.0 40.0 33.0 40.0 14-15 37.258125 37.0 37.0 40.0 33.0 40.0 16-17 37.0815 37.0 37.0 40.0 33.0 40.0 18-19 37.213 37.0 37.0 40.0 33.0 40.0 20-21 37.433125 37.0 37.0 40.0 33.0 40.0 22-23 37.197125 37.0 37.0 40.0 33.0 40.0 24-25 37.28125 37.0 37.0 40.0 33.0 40.0 26-27 36.99275 37.0 37.0 40.0 33.0 40.0 28-29 37.193 37.0 37.0 40.0 33.0 40.0 30-31 37.16137500000001 37.0 37.0 40.0 33.0 40.0 32-33 37.059 37.0 37.0 40.0 33.0 40.0 34-35 36.873 37.0 37.0 40.0 33.0 40.0 36-37 36.78125 37.0 37.0 40.0 33.0 40.0 38-39 36.60325 37.0 37.0 40.0 33.0 40.0 40-41 36.508125 37.0 37.0 40.0 33.0 40.0 42-43 36.423125 37.0 37.0 40.0 33.0 40.0 44-45 36.147125 37.0 37.0 37.0 33.0 40.0 46-47 36.070375 37.0 37.0 37.0 33.0 40.0 48-49 35.86175 37.0 35.0 37.0 33.0 40.0 50-51 35.64275 37.0 33.0 37.0 33.0 40.0 52-53 35.50325 37.0 33.0 37.0 33.0 40.0 54-55 35.4675 37.0 33.0 37.0 33.0 37.0 56-57 35.30675 37.0 33.0 37.0 33.0 37.0 58-59 34.883875 37.0 33.0 37.0 33.0 37.0 60-61 34.814750000000004 37.0 33.0 37.0 33.0 37.0 62-63 34.792875 37.0 33.0 37.0 33.0 37.0 64-65 34.310625 37.0 33.0 37.0 30.0 37.0 66-67 34.279375 37.0 33.0 37.0 30.0 37.0 68-69 32.959125 35.0 33.0 35.0 27.0 37.0 70-71 33.285397323661826 33.0 33.0 37.0 27.0 37.0 72-73 33.97848123467648 37.0 33.0 37.0 27.0 37.0 74-75 34.33458075584555 37.0 33.0 37.0 33.0 37.0 76-77 34.15421119138705 37.0 33.0 37.0 30.0 37.0 78-79 34.133002332864116 37.0 33.0 37.0 30.0 37.0 80-81 34.07165212450286 37.0 33.0 37.0 27.0 37.0 82-83 33.880542262102864 37.0 33.0 37.0 27.0 37.0 84-85 33.86732489785783 37.0 33.0 37.0 27.0 37.0 86-87 33.76337033299697 35.0 33.0 37.0 27.0 37.0 88-89 33.72628657921292 35.0 33.0 37.0 27.0 37.0 90-91 33.546291624621595 33.0 33.0 37.0 27.0 37.0 92-93 33.28279515640767 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 10.0 22 7.0 23 8.0 24 13.0 25 15.0 26 29.0 27 37.0 28 45.0 29 61.0 30 74.0 31 108.0 32 151.0 33 209.0 34 272.0 35 525.0 36 1005.0 37 1057.0 38 367.0 39 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.9 2.75 2.45 4.9 2 75.23142356767576 15.161371028271203 5.604203152364273 4.003002251688766 3 38.0 38.15 13.125 10.725 4 35.699999999999996 28.9 17.1 18.3 5 25.6 32.725 23.825 17.849999999999998 6 20.625 38.35 24.9 16.125 7 36.05 27.575 18.975 17.4 8 31.175000000000004 28.799999999999997 22.875 17.150000000000002 9 26.35 27.700000000000003 27.325 18.625 10-11 26.187500000000004 26.987499999999997 26.5 20.325 12-13 28.487499999999997 26.337500000000002 25.5625 19.6125 14-15 23.525 30.8 27.625 18.05 16-17 25.0375 31.2 24.962500000000002 18.8 18-19 25.2 26.75 25.087500000000002 22.9625 20-21 24.762500000000003 27.700000000000003 26.575 20.962500000000002 22-23 26.700000000000003 23.400000000000002 26.987499999999997 22.912499999999998 24-25 27.537499999999998 23.3875 27.200000000000003 21.875 26-27 25.837500000000002 26.325 28.3375 19.5 28-29 26.0125 26.450000000000003 25.8125 21.725 30-31 28.849999999999998 26.0125 24.05 21.087500000000002 32-33 24.3625 28.3625 26.05 21.224999999999998 34-35 25.9875 23.8125 27.6375 22.5625 36-37 25.7625 22.650000000000002 28.9375 22.650000000000002 38-39 26.387500000000003 24.337500000000002 30.349999999999998 18.925 40-41 27.187499999999996 25.624999999999996 25.124999999999996 22.0625 42-43 25.025 28.175 25.5375 21.2625 44-45 24.7 24.8125 27.275 23.2125 46-47 25.2375 22.3125 26.825 25.624999999999996 48-49 25.124999999999996 24.175 30.2625 20.4375 50-51 26.2875 25.424999999999997 28.625 19.662499999999998 52-53 25.5625 27.462500000000002 25.974999999999998 21.0 54-55 24.0375 28.749999999999996 27.1375 20.075000000000003 56-57 26.6625 24.462500000000002 28.1875 20.6875 58-59 24.625 23.1875 29.362500000000004 22.825 60-61 24.425 23.5625 29.1375 22.875 62-63 23.5375 27.425 30.2 18.8375 64-65 25.05 25.7875 27.975 21.1875 66-67 25.5125 26.9125 27.125 20.45 68-69 23.95 27.275 26.5625 22.2125 70-71 27.019254813703427 23.74343585896474 27.04426106526632 22.193048262065513 72-73 25.89162808159179 24.014516330872233 27.49343010887248 22.600425478663496 74-75 23.772545090180362 27.45490981963928 27.580160320641284 21.19238476953908 76-77 23.611285266457678 25.9435736677116 27.849529780564264 22.595611285266457 78-79 25.22579026593076 22.96788760662318 30.230807827395882 21.575514300050173 80-81 24.97172301118512 26.366721126052532 29.131582254618575 19.529973608143774 82-83 24.76706119365399 24.18786199949635 29.12364643666583 21.921430370183835 84-85 24.735116044399597 23.107971745711403 30.02018163471241 22.13673057517659 86-87 22.616044399596365 26.60191725529768 31.15539858728557 19.62663975782038 88-89 23.145812310797176 28.43087790110999 29.603935418768923 18.819374369323917 90-91 27.459636730575177 24.848637739656912 28.43087790110999 19.26084762865792 92-93 23.284561049445003 27.547931382441977 28.784056508577194 20.383451059535822 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 4.5 18 5.0 19 1.0 20 4.0 21 4.5 22 4.0 23 3.5 24 3.0 25 5.5 26 6.0 27 7.0 28 12.0 29 16.5 30 22.0 31 25.5 32 27.5 33 49.5 34 57.5 35 61.5 36 74.0 37 89.0 38 118.5 39 137.0 40 156.0 41 188.0 42 203.5 43 199.5 44 193.5 45 167.5 46 221.5 47 247.0 48 198.0 49 183.0 50 165.0 51 154.5 52 161.5 53 185.5 54 154.5 55 102.0 56 80.0 57 70.5 58 68.5 59 61.0 60 55.5 61 51.5 62 46.5 63 42.5 64 42.5 65 37.0 66 24.0 67 23.5 68 23.0 69 15.5 70 10.0 71 7.0 72 6.5 73 6.0 74 4.5 75 2.5 76 1.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.075 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.025220680958385876 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 2.0 71 2.0 72 1.0 73 1.0 74 4.0 75 2.0 76 1.0 77 0.0 78 2.0 79 4.0 80 5.0 81 2.0 82 6.0 83 2.0 84 2.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3964.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.43483788938335 72.7 2 4.545454545454546 7.1499999999999995 3 0.9853782581055308 2.325 4 0.6357279084551812 2.0 5 0.3814367450731087 1.5 6 0.12714558169103624 0.6 7 0.12714558169103624 0.7000000000000001 8 0.1589319771137953 1.0 9 0.03178639542275906 0.22499999999999998 >10 0.5085823267641449 8.825 >50 0.06357279084551812 2.9749999999999996 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 64 1.6 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 55 1.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 45 1.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 44 1.0999999999999999 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 28 0.7000000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 28 0.7000000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 26 0.65 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 23 0.575 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 21 0.525 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 19 0.475 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 15 0.375 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 13 0.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTAT 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 7 0.17500000000000002 No Hit GGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAGTTTTTCTTA 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCA 5 0.125 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0125 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGACATC 35 3.5943624E-4 50.27848 1 GCTCGTG 30 0.0054144408 29.329115 80-81 GTGAAGG 30 0.0054144408 29.329115 84-85 TTGCTCG 30 0.005586226 29.144653 78-79 GAAGGTA 30 0.005762292 28.9625 86-87 >>END_MODULE Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142659 READS because READLEN < 1 Read 142659 spots for ERR6133425.sra Written 142659 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra Rejected 142654 READS because READLEN < 1 Read 142654 spots for ERR6133425.sra Written 142654 spots for ERR6133425.sra SRR ids: ['ERR6133425.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7ifpg1td ERR6133425.sra spots: 2853085 blocks: [[1, 142654], [142655, 285308], [285309, 427962], [427963, 570616], [570617, 713270], [713271, 855924], [855925, 998578], [998579, 1141232], [1141233, 1283886], [1283887, 1426540], [1426541, 1569194], [1569195, 1711848], [1711849, 1854502], [1854503, 1997156], [1997157, 2139810], [2139811, 2282464], [2282465, 2425118], [2425119, 2567772], [2567773, 2710426], [2710427, 2853085]] ERR6133425 file size 631884 ERR6133425 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o ERR6133425 ERR6133425_1.fastq Input file: ERR6133425_1.fastq trimmed: ERR6133425-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 04:58:37 2024 >> started Sat Dec 7 04:58:41 2024 >> done (4.478s) 2853085 reads processed; of these: 1672 ( 0.06%) short reads filtered out after trimming by size control 49 ( 0.00%) empty reads filtered out after trimming by size control 2851364 (99.94%) reads available; of these: 38447 ( 1.35%) trimmed reads available after processing 2812917 (98.65%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 29 0.00% 19 25 0.00% 20 15 0.00% 21 17 0.00% 22 19 0.00% 23 10 0.00% 24 8 0.00% 25 8 0.00% 26 8 0.00% 27 3 0.00% 28 8 0.00% 29 27 0.00% 30 4 0.00% 31 6 0.00% 32 8 0.00% 33 28 0.00% 34 7 0.00% 35 4 0.00% 36 2 0.00% 37 11 0.00% 38 8 0.00% 39 12 0.00% 40 13 0.00% 41 14 0.00% 42 11 0.00% 43 46 0.00% 44 17 0.00% 45 23 0.00% 46 18 0.00% 47 21 0.00% 48 26 0.00% 49 17 0.00% 50 20 0.00% 51 24 0.00% 52 14 0.00% 53 18 0.00% 54 31 0.00% 55 22 0.00% 56 18 0.00% 57 12 0.00% 58 18 0.00% 59 17 0.00% 60 19 0.00% 61 16 0.00% 62 2 0.00% 63 0 0.00% 64 4 0.00% 65 6 0.00% 66 3 0.00% 67 5 0.00% 68 11 0.00% 69 28 0.00% 70 2951 0.10% 71 2279 0.08% 72 2352 0.08% 73 2212 0.08% 74 2524 0.09% 75 2335 0.08% 76 2042 0.07% 77 2097 0.07% 78 2488 0.09% 79 3136 0.11% 80 2437 0.09% 81 2436 0.09% 82 2944 0.10% 83 3277 0.11% 84 2522 0.09% 85 79 0.00% 86 165 0.01% 87 261 0.01% 88 447 0.02% 89 914 0.03% 90 2241 0.08% 91 6546 0.23% 92 26408 0.93% 93 2775510 97.34% 2851364 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.32 fanout-score-rank=28 prefix-density=0.53 prefix-fanout=2.1 sequence=TGTACATTTGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=37.09 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.1 sequence=AGAAACAAATCCACTATTGGTTTTACGTCAAGCAATACGTAGAGTAACTCCCAATATAGGAGTAAAAACAAGACGTAATAAAAAAGGATCGACGCGGAAAGTTCCGATTGAAATAGGATCTAAACAAGGAAGAGCACTTGCCATTCGTTGGTTATTAGAAGCATCCCAAAAGCGTCCGGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCAAAGGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAATAGAGCTCTTGCACATTTTCGTTAATCCATGAACAGAATCTAGGTATGTAGACACATGGATCCATACATCTCGATCGGAAAAGAATCAAT Started job on | Dec 07 04:59:01 Started mapping on | Dec 07 04:59:01 Finished on | Dec 07 04:59:23 Mapping speed, Million of reads per hour | 466.59 Number of input reads | 2851364 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2047926 Uniquely mapped reads % | 71.82% Average mapped length | 92.43 Number of splices: Total | 134872 Number of splices: Annotated (sjdb) | 115343 Number of splices: GT/AG | 130557 Number of splices: GC/AG | 2798 Number of splices: AT/AC | 50 Number of splices: Non-canonical | 1467 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.04% Deletion average length | 1.87 Insertion rate per base | 0.03% Insertion average length | 2.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 751375 % of reads mapped to multiple loci | 26.35% Number of reads mapped to too many loci | 7024 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.56% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 52063 52063 52063 N_multimapping 751375 751375 751375 N_noFeature 107053 126816 1960135 N_ambiguous 75168 7227 241 UnstrandedReadsAssigned:1865705 PositiveStrandReadsAssigned:1913883 NegativeStrandReadsAssigned:87550 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133425 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133425-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,851,364 reads, 2,500,667 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 951 rounds 52973 ERR6133425.ke.tsv 35125 ERR6133425.se.tsv 88098 total ==> ERR6133425.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 41 15.9528 PNS24243 293 194 0 0 KQK14069 1603 1504 31 11.0032 KQK14071 474 375 0 0 ==> ERR6133425.se.tsv <== BRADI_1g14170v3 32 BRADI_1g53295v3 13 BRADI_1g59795v3 19 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 36 BRADI_1g74790v3 24 BRADI_1g09890v3 0 BRADI_1g77505v3 35 BRADI_1g48960v3 0 ERR6133425 completed mapping pipeline successfully